Maryland’s rivers once teemed with a fish called river herring, the generic name for alewife and blueback herring.

A century ago, watermen on the Choptank River caught millions of these fish that live in the ocean, but return to fresh water to spawn in a single year.

But the population has plummeted, thanks to overfishing, dams that block their paths upstream to spawning grounds and habitat loss.

And that’s bad news not only for the watermen, but the striped bass, osprey and other critters that feed on these tiny creatures not much bigger than your cell phone.

Scientists who have been studying their decline have used a lot of tricks in their bags.

They’ve waded into the water with dip nets to catch eggs and larvae. But fish eggs are hard to tell apart. And you have to pick through a wet mass of dead leaves and muck to find them.

They’ve tried sending electrical pulses through the water and scooping up the stunned fish that float to the surface. But electrofishing requires several people, and it doesn’t work well in streams that are too deep or too wide.

They’ve used sonar, basically a fancy underwater fish finder. But one unit costs around $90,000 dollars, and it must stay in one place all season.

And none of those methods are ideal if you want to study a lot of streams quickly. But there’s a new method that is. You simply fill a plastic bottle with river water and send it to a genetics lab.

That’s because fish leave behind eggs, waste, and slime as they swim. It all contains DNA. A geneticist can figure out which species that DNA came from.

There’s no way to know if it came from ten little fish or one big fish. But you can see whether river herring are there, and whether there seem to be more in one place than another.

Biologist Matt Ogburn of the Smithsonian Environmental Research Center says that can be really helpful.

"We’re hoping to find out what habitats and what places are most important for river herring to spawn so we can help rebuild their populations," he explained. "So it was something that we recognized early on that we would want an efficient way to sample a lot of sites."

Ogburn is among the first to use environmental DNA, or eDNA, in the Chesapeake Bay watershed. He’s using it to create a map of where river herring are spawning throughout the region. That takes some serious sampling.

They’ve worked in the York, the James and the Rappahannock rivers in Virginia, the Potomac and a host of rivers and streams in Maryland; the Patuxent, the Patapsco, the Gunpowder, the Northeast, Deer Creek, the Elk River, the Bohemia, the Sassafras, the Choptank, the Nanticoke, the Pocomoke and on and on over the last three years.

Because eDNA sampling is so simple, they could monitor more than 200 sites. But at first, even the geneticist who decoded the samples wasn’t sure it would work.

Louis Plough, of the University of Maryland Center for Environmental Science's Horn Point Laboratory, says it wasn’t until they were a year into the project "that I was like 'Oh man, this IS working.' You know, we’re skeptical scientists and we were as surprised as anyone that it worked so well."

The samples indicate that alewife seem to prefer the Bay’s eastern shore, and blueback herring the western. Now Matt Ogburn is analyzing the data to better understand each species’ preferences.

"In the past, they’ve sort of been managed as a group," he says. "But they are different species that have different behaviors and probably different conservation and restoration needs."

All that doesn’t mean Ogburn will be tossing his nets and sonar equipment anytime soon. Sometimes, he says, eDNA isn’t the right tool. But when it is, it sure beats trying to find the actual fish.

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